ARID2

gene
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Also known as KIAA1557DKFZp686G052FLJ30619BAF200SMARCF3ZIPZAPp200

Summary

ARID2 (AT-rich interaction domain 2, HGNC:18037) is a protein-coding gene on chromosome 12q12, encoding AT-rich interactive domain-containing protein 2 (Q68CP9). Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). It is a selective cancer dependency (DepMap: 33.9% of cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This gene encodes a member of the AT-rich interactive domain (ARID)-containing family of DNA-binding proteins. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. This protein functions as a subunit of the polybromo- and BRG1-associated factor or PBAF (SWI/SNF-B) chromatin remodeling complex which facilitates ligand-dependent transcriptional activation by nuclear receptors. Mutations in this gene are associated with hepatocellular carcinomas. A pseudogene of this gene is found on chromosome1.

Source: NCBI Gene 196528 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Coffin-Siris syndrome (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 16
  • Clinical variants (ClinVar): 585 total — 76 pathogenic, 35 likely-pathogenic
  • Phenotypes (HPO): 103
  • Druggable target: yes
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 21 cancer types
  • Cancer dependency (DepMap): dependent in 33.9% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_152641

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18037
Approved symbolARID2
NameAT-rich interaction domain 2
Location12q12
Locus typegene with protein product
StatusApproved
AliasesKIAA1557, DKFZp686G052, FLJ30619, BAF200, SMARCF3, ZIPZAP, p200
Ensembl geneENSG00000189079
Ensembl biotypeprotein_coding
OMIM609539
Entrez196528

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000334344, ENST00000422737, ENST00000426776, ENST00000427628, ENST00000444670, ENST00000457135, ENST00000477947, ENST00000479608, ENST00000480128, ENST00000700074, ENST00000851072, ENST00000859902, ENST00000859903, ENST00000956309

RefSeq mRNA: 2 — MANE Select: NM_152641 NM_001347839, NM_152641

CCDS: CCDS31783

Canonical transcript exons

ENST00000334344 — 21 exons

ExonStartEnd
ENSE000012387464583674145836991
ENSE000014201314582142045821487
ENSE000014265584583658945836655
ENSE000034602594589342045893543
ENSE000034685814589363045893721
ENSE000034862164581141845811551
ENSE000034920034589201145892096
ENSE000035180234583932945839496
ENSE000035183064584883645848970
ENSE000035216424584685645846937
ENSE000035239004581767045817888
ENSE000035323084584958045849776
ENSE000035406074583749845837707
ENSE000035610164583732145837417
ENSE000035648784586080145860949
ENSE000035904724585003645852896
ENSE000036722624589178045891918
ENSE000038436394590493445908037
ENSE000039787634573004445730137
ENSE000039787644573121745731314
ENSE000042836444572970645729928

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 95.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.5302 / max 146.6726, expressed in 1751 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1251526.09951583
1251502.87601350
1251511.2583600
1251550.5199146
1251530.5139272
1251540.215597
1251600.04714

Top tissues by expression

255 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001995.74gold quality
pancreatic ductal cellCL:000207994.91gold quality
secondary oocyteCL:000065594.44gold quality
oocyteCL:000002390.93gold quality
bone marrow cellCL:000209290.50gold quality
kidney epitheliumUBERON:000481989.90silver quality
thymusUBERON:000237089.68gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.50gold quality
oviduct epitheliumUBERON:000480488.29gold quality
ventricular zoneUBERON:000305388.23gold quality
nasal cavity epitheliumUBERON:000538487.69silver quality
colonic epitheliumUBERON:000039787.54gold quality
ganglionic eminenceUBERON:000402387.43gold quality
trabecular bone tissueUBERON:000248387.41gold quality
calcaneal tendonUBERON:000370187.06gold quality
bone marrowUBERON:000237186.98gold quality
ileal mucosaUBERON:000033186.87gold quality
nippleUBERON:000203086.78gold quality
lower esophagus mucosaUBERON:003583486.59gold quality
tibialis anteriorUBERON:000138586.54silver quality
adrenal tissueUBERON:001830386.33gold quality
sural nerveUBERON:001548885.93gold quality
tonsilUBERON:000237285.81gold quality
testisUBERON:000047385.66gold quality
mucosa of paranasal sinusUBERON:000503085.24gold quality
epithelium of nasopharynxUBERON:000195185.10gold quality
cardia of stomachUBERON:000116285.05gold quality
corpus callosumUBERON:000233684.91gold quality
left testisUBERON:000453384.85gold quality
cortical plateUBERON:000534384.72gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

309 targeting ARID2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-1193100.0065.93529
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5692A100.0074.406850
HSA-MIR-432-3P100.0067.86705
HSA-MIR-188-3P100.0068.761240
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-607799.9968.042299
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-366299.9973.825684
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-480399.9871.993117
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-60799.9773.625593
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-9-3P99.9670.882068

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 33.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 34)

  • zipzap may serve as a transcription co-activator for the regulation of cardiac gene expression (PMID:16782067)
  • 18.2% of individuals with HCV-associated HCC in the United States and Europe harbored ARID2 inactivation mutations, suggesting that ARID2 is a tumor suppressor gene that is relatively commonly mutated in this tumor subtype. (PMID:21822264)
  • we summarize the current knowledge about the relevance of ARID2 in Hepatocellular carcinoma and the implication in future patient care (PMID:22095441)
  • Recurrent inactivating mutations of ARID2 is associated with non-small cell lung carcinoma. (PMID:23047306)
  • Mutations in ARID2 gene is associated with microsatellite unstable colorectal cancer. (PMID:24382590)
  • The subsequent validation study on 68 LCBs identified recurrent mutations in TERT promoter, chromatin regulators (BAP1, PBRM1 and ARID2), a synapse organization gene (PCLO), IDH genes and KRAS. (PMID:25636086)
  • loss of ARID2 protein expression may be associated with recurrence of hepatocellular carcinoma (PMID:25701229)
  • This is the first report of mutations in ARID2 associated with developmental delay and intellectual disabilities . (PMID:26238514)
  • Arid2 role in genome-wide transcriptional regulation by SWI/SNF complexes. (PMID:26716708)
  • These findings highlight the potential role of ARID2 as a tumor growth suppressor in hepatocellular carcinoma (PMID:27351279)
  • study identifies mutations in the ARID2 gene as a novel and rare cause for a CSS-like phenotype and enlarges the list of CSS-like genes (PMID:28124119)
  • ARID2 knockout could contribute to disruption of DNA repair process. (PMID:28238438)
  • Baf200 and Rad51 are present in the same complex and that this interaction is mediated by C-terminal sequences in both proteins. (PMID:28381560)
  • We present a 4-year-old girl with delayed neuromotor development, short stature of prenatal onset, and specific behavioral and craniofacial features harboring an intragenic deletion in the ARID2 gene. The phenotype confirmed the major features of the recently described ARID2-related intellectual disability syndrome. (PMID:28884947)
  • Mutations in or involving the ARID2 gene were identified in the patients with the features resembling Coffin-Siris syndrome. (PMID:29698805)
  • The binding between HBc and BAF200 was of vital importance to HBc mediated downregulation of interferon-induced transmembrane protein 1 (IFITM1) expression. (PMID:31075894)
  • Long non-coding RNA Arid2-IR affects advanced glycation end products-induced human retinal endothelial cell injury by binding to Smad3. (PMID:31912402)
  • Association between ARID2 and RAS-MAPK pathway in intellectual disability and short stature. (PMID:33051312)
  • Exome sequencing identifies ARID2 as a novel tumor suppressor in early-onset sporadic rectal cancer. (PMID:33262464)
  • ARID2 Deficiency Correlates with the Response to Immune Checkpoint Blockade in Melanoma. (PMID:33333124)
  • Expression and prognostic values of ARID family members in breast cancer. (PMID:33592583)
  • ARID2 deficiency promotes tumor progression and is associated with higher sensitivity to chemotherapy in lung cancer. (PMID:33742126)
  • CREB1 acts via the miR922/ARID2 axis to enhance malignant behavior of liver cancer cells. (PMID:33786634)
  • ARID1A, ARID1B, and ARID2 Mutations Serve as Potential Biomarkers for Immune Checkpoint Blockade in Patients With Non-Small Cell Lung Cancer. (PMID:34512623)
  • BRD4 inhibition induces synthetic lethality in ARID2-deficient hepatocellular carcinoma by increasing DNA damage. (PMID:35017665)
  • Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. (PMID:35385731)
  • ARID2 suppression promotes tumor progression and upregulates cytokeratin 8, 18 and beta-4 integrin expression in TP53-mutated tobacco-related oral cancer and has prognostic implications. (PMID:35869277)
  • miR-29a-5p regulates the malignant biological process of liver cancer cells through ARID2 regulation of EMT. (PMID:36530029)
  • USP2 Inhibits Lung Cancer Pathogenesis by Reducing ARID2 Protein Degradation via Ubiquitination. (PMID:36567903)
  • ARID2, a rare cause of Coffin-Siris syndrome: A novel microdeletion at 12q12q13.11 causing severe short stature and literature review. (PMID:36756859)
  • Coffin-Siris Syndrome: Case Series of Three Patients and a Novel ARID2 Variant. (PMID:38182156)
  • ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals. (PMID:38243407)
  • ARID2 mutations may relay a distinct subset of cutaneous melanoma patients with different outcomes. (PMID:38341515)
  • Revealing the clinical impact of MTOR and ARID2 gene mutations on MALT lymphoma of the alimentary canal using targeted sequencing. (PMID:39054516)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioarid2ENSDARG00000007413
mus_musculusArid2ENSMUSG00000033237
rattus_norvegicusArid2ENSRNOG00000004831
drosophila_melanogasterBap170FBGN0042085
caenorhabditis_elegansWBGENE00007433

Protein

Protein identifiers

AT-rich interactive domain-containing protein 2Q68CP9 (reviewed: Q68CP9)

Alternative names: BRG1-associated factor 200, Zinc finger protein with activation potential, Zipzap/p200

All UniProt accessions (6): A0A087WY37, A0A8V8TP93, F8VWP4, F8W108, F8WCU9, Q68CP9

UniProt curated annotations — full annotation on UniProt →

Function. Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Required for the stability of the SWI/SNF chromatin remodeling complex SWI/SNF-B (PBAF). May be involved in targeting the complex to different genes. May be involved in regulating transcriptional activation of cardiac genes.

Subunit / interactions. Component of the SWI/SNF-B (PBAF) chromatin remodeling complex, at least composed of SMARCA4/BRG1, SMARCB1/BAF47/SNF5, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, perhaps SMARCD3/BAF60C, SMARCC1/BAF155, SMARCC2/BAF170, PBRM1/BAF180, ARID2/BAF200 and actin. Interacts with SRF. Forms complexes with SRF and SRF cofactors MYOCD, NKX2-5 and SRFBP1.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in heart.

Disease relevance. Coffin-Siris syndrome 6 (CSS6) [MIM:617808] A form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. Both autosomal dominant and autosomal recessive inheritance patterns have been reported. CSS6 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt IDNamesCanonical?
Q68CP9-11yes
Q68CP9-32

RefSeq proteins (2): NP_001334768, NP_689854* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001606ARID_domDomain
IPR003150DNA-bd_RFXDomain
IPR013087Znf_C2H2_typeDomain
IPR016024ARM-type_foldHomologous_superfamily
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily
IPR036431ARID_dom_sfHomologous_superfamily
IPR052406Chromatin_Remodeling_CompFamily

Pfam: PF01388, PF02257

UniProt features (106 total): helix 30, sequence conflict 18, modified residue 10, compositionally biased region 9, region of interest 8, turn 8, strand 7, cross-link 7, sequence variant 2, initiator methionine 1, chain 1, short sequence motif 1, domain 1, DNA-binding region 1, zinc finger region 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
7VDVELECTRON MICROSCOPY3.4
7Y8RELECTRON MICROSCOPY4.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q68CP9-F152.300.16

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (17): 2, 4, 631, 635, 653, 689, 692, 1300, 1391, 1496, 7, 15, 119, 555, 1701, 1716, 1731

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

IDPathway
R-HSA-3214858RMTs methylate histone arginines
R-HSA-8939243RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-9933939Formation of the polybromo-BAF (pBAF) complex
R-HSA-212436Generic Transcription Pathway
R-HSA-3247509Chromatin modifying enzymes
R-HSA-4839726Chromatin organization
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74160Gene expression (Transcription)
R-HSA-8878171Transcriptional regulation by RUNX1

MSigDB gene sets: 600 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_CHROMOSOME_ORGANIZATION, GOBP_REGULATION_OF_DNA_RECOMBINATION, WANG_CLIM2_TARGETS_UP, GOBP_MUSCLE_TISSUE_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_HEMOPOIESIS, GOBP_CORONARY_VASCULATURE_DEVELOPMENT, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_GROWTH, chr12q12, TATTATA_MIR374, GOBP_ARTERY_DEVELOPMENT, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR_VIA_HOMOLOGOUS_RECOMBINATION, GOBP_MUSCLE_CELL_PROLIFERATION

GO Biological Process (22): heart morphogenesis (GO:0003007), nucleosome disassembly (GO:0006337), chromatin remodeling (GO:0006338), regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of cell population proliferation (GO:0008285), regulation of mitotic metaphase/anaphase transition (GO:0030071), negative regulation of cell migration (GO:0030336), homeostatic process (GO:0042592), positive regulation of T cell differentiation (GO:0045582), positive regulation of cell differentiation (GO:0045597), positive regulation of myoblast differentiation (GO:0045663), embryonic organ development (GO:0048568), cardiac muscle cell proliferation (GO:0060038), coronary artery morphogenesis (GO:0060982), regulation of G0 to G1 transition (GO:0070316), positive regulation of double-strand break repair via homologous recombination (GO:1905168), regulation of G1/S transition of mitotic cell cycle (GO:2000045), positive regulation of double-strand break repair (GO:2000781), regulation of nucleotide-excision repair (GO:2000819), chromatin organization (GO:0006325), regulation of DNA-templated transcription (GO:0006355), circulatory system development (GO:0072359)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (8): kinetochore (GO:0000776), chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), plasma membrane (GO:0005886), nuclear matrix (GO:0016363), SWI/SNF complex (GO:0016514), RSC-type complex (GO:0016586)

Reactome top-level categories

Rollup of top-7 pathways:

CategoryPathways
Chromatin modifying enzymes1
Transcriptional regulation by RUNX11
SWI/SNF chromatin remodelers1
RNA Polymerase II Transcription1
Chromatin organization1
Gene expression (Transcription)1
Generic Transcription Pathway1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
regulation of mitotic cell cycle phase transition2
nuclear lumen2
SWI/SNF superfamily-type complex2
heart development1
animal organ morphogenesis1
protein-DNA complex disassembly1
nucleosome organization1
chromatin organization1
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
cell population proliferation1
regulation of cell population proliferation1
negative regulation of cellular process1
metaphase/anaphase transition of mitotic cell cycle1
regulation of metaphase/anaphase transition of cell cycle1
cell migration1
regulation of cell migration1
negative regulation of cell motility1
biological_process1
T cell differentiation1
regulation of T cell differentiation1
positive regulation of lymphocyte differentiation1
positive regulation of T cell activation1
cell differentiation1
regulation of cell differentiation1
positive regulation of cellular process1
positive regulation of developmental process1
myoblast differentiation1
positive regulation of cell differentiation1
regulation of myoblast differentiation1
embryo development1
animal organ development1
striated muscle cell proliferation1
cardiac muscle tissue growth1
artery morphogenesis1
coronary vasculature morphogenesis1
regulation of cell cycle process1
G0 to G1 transition1
double-strand break repair via homologous recombination1

Protein interactions and networks

STRING

1775 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ARID2PBRM1Q86U86999
ARID2BRD7Q9NPI1997
ARID2SMARCA4P51532996
ARID2SMARCB1Q12824995
ARID2PHF10Q8WUB8995
ARID2SMARCE1Q969G3992
ARID2ARID1AO14497989
ARID2ARID1BQ8NFD5985
ARID2SMARCC1Q92922964
ARID2SMARCC2Q8TAQ2945
ARID2BRD9Q9H8M2933
ARID2ACTL6AO96019932
ARID2DPF2Q92785929
ARID2SMARCA2P51531925
ARID2ACTL6BO94805836

IntAct

165 interactions, top by confidence:

ABTypeScore
SMARCB1ARID2psi-mi:“MI:0915”(physical association)0.890
SMARCB1ARID1Apsi-mi:“MI:0914”(association)0.860
SMARCE1ARID1Apsi-mi:“MI:0914”(association)0.840
NUP50KPNA4psi-mi:“MI:0914”(association)0.830
PBRM1SMARCA4psi-mi:“MI:0914”(association)0.800
SMARCE1ARID2psi-mi:“MI:0915”(physical association)0.800
SMARCC1ARID1Apsi-mi:“MI:0914”(association)0.790
SMARCD1ARID1Apsi-mi:“MI:0914”(association)0.790
SMARCC2ARID1Apsi-mi:“MI:0914”(association)0.790
ARID2SMARCA4psi-mi:“MI:0915”(physical association)0.770
ARID2SMARCA4psi-mi:“MI:0914”(association)0.770
SS18ARID1Apsi-mi:“MI:0914”(association)0.760
SMARCE1SMARCA2psi-mi:“MI:0914”(association)0.730
SMARCA4ACTL6Apsi-mi:“MI:0914”(association)0.670

BioGRID (250): ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Co-fractionation), ARID2 (Co-fractionation), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), ARID2 (Affinity Capture-MS)

ESM2 similar proteins: A9LNK9, B2D6P4, E9Q7E2, G4N3L5, G5ED29, O15350, O45211, O61707, O95104, P14003, P15330, P20227, P23645, P29303, P34545, P47238, P49880, P53361, P98149, Q02926, Q0DA50, Q1LZF1, Q21955, Q22366, Q22703, Q29A33, Q3L1C9, Q4V3C1, Q61L47, Q68CP9, Q6C7K8, Q6E2N3, Q6YGZ4, Q7TSH6, Q7ZX03, Q8QGQ6, Q8SWR8, Q91YA8, Q91YB0, Q91YB2

Diamond homologs: A0A0K3AXH1, A2BEA6, A2CG63, A6NKF2, A6PWV5, E1BLP6, E2R9X2, E7F888, E9Q7E2, F8VPQ2, O13953, O74365, P29374, Q03989, Q14865, Q24573, Q3SWY1, Q3U108, Q4H3P5, Q4LE39, Q4V3E2, Q54RM0, Q5XGD9, Q5ZJ69, Q62431, Q68CP9, Q6GQD7, Q8BM75, Q8IN94, Q8IVW6, Q8MQH7, Q94C32, Q99856, Q9JKB5, Q9Z1N7, C0SUW7, Q0WNR6, Q940Y3, Q9LTT3, Q9SGS2

SIGNOR signaling

2 interactions.

AEffectBMechanism
ARID2“form complex”“SWI/SNF complex”binding
ARID2“form complex”“SWI/SNF ACTL6B varian”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 148 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Formation of the canonical BAF (cBAF) complex1380.9×1e-21
Formation of the polybromo-BAF (pBAF) complex1380.9×1e-21
Formation of the embryonic stem cell BAF (esBAF) complex1376.6×3e-21
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)1671.7×5e-25
Formation of the non-canonical BAF (ncBAF) complex1065.9×2e-15
Regulation of endogenous retroelements1450.6×2e-19
Regulation of MITF-M-dependent genes involved in pigmentation1744.3×3e-22
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known1132.4×8e-13

GO biological processes:

GO termPartnersFoldFDR
regulation of G0 to G1 transition1681.1×1e-25
regulation of nucleotide-excision repair1672.4×1e-24
regulation of mitotic metaphase/anaphase transition1659.6×4e-23
nucleosome disassembly848.3×2e-10
positive regulation of double-strand break repair1641.4×4e-20
positive regulation of T cell differentiation1241.1×5e-15
regulation of G1/S transition of mitotic cell cycle1636.9×3e-19
NLS-bearing protein import into nucleus636.2×7e-07

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 21 cancer types — CHOL, CSCC, ESCA, ESCC, GB, GBC, HCC, HNSC, LGGNOS, LUAD, MBL, MEL…(+9 more).

Clinical variants and AI predictions

ClinVar

585 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic76
Likely pathogenic35
Uncertain significance285
Likely benign111
Benign21

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1034327NM_152641.4(ARID2):c.5026C>T (p.Gln1676Ter)Pathogenic
1170954NM_152641.4(ARID2):c.118dup (p.Val40fs)Pathogenic
1170956NM_152641.4(ARID2):c.2401_2402del (p.Met801fs)Pathogenic
1170957NM_152641.4(ARID2):c.3301_3302insAGGT (p.Val1101fs)Pathogenic
1170958NM_152641.4(ARID2):c.3814C>T (p.Arg1272Ter)Pathogenic
1170959NM_152641.4(ARID2):c.4732C>T (p.Gln1578Ter)Pathogenic
1170960NM_152641.3:c.(705+1_706-1)_(1330+1_1331-1)delPathogenic
1170961GRCh37/hg19 12q12(chr12:46168172-46304719)x1Pathogenic
1170962GRCh37/hg19 12q12(chr12:46150008-46321670)x1Pathogenic
1177333NM_152641.4(ARID2):c.156_157del (p.Arg53fs)Pathogenic
1177334NM_152641.4(ARID2):c.1262_1265dup (p.Tyr423fs)Pathogenic
1177336NM_152641.4(ARID2):c.1580+1G>APathogenic
1177337NM_152641.4(ARID2):c.2458C>T (p.Gln820Ter)Pathogenic
1196352NM_152641.4(ARID2):c.5029C>T (p.Arg1677Ter)Pathogenic
1198066NM_152641.4(ARID2):c.5132_5135dup (p.Ser1713fs)Pathogenic
1285520NM_152641.4(ARID2):c.4540_4541delinsGAA (p.Thr1514fs)Pathogenic
1321937NM_152641.4(ARID2):c.2734C>T (p.Gln912Ter)Pathogenic
1343246NM_152641.4(ARID2):c.1331-1G>CPathogenic
1526286NC_000012.12:g.45690000_45750000delPathogenic
1675488NM_152641.4(ARID2):c.3065dup (p.Pro1023fs)Pathogenic
1679288NM_152641.4(ARID2):c.4210dup (p.Gln1404fs)Pathogenic
1684625NM_152641.4(ARID2):c.2377C>T (p.Gln793Ter)Pathogenic
1699019NM_152641.4(ARID2):c.4255_4256del (p.Pro1419fs)Pathogenic
1710278NM_152641.4(ARID2):c.675G>A (p.Trp225Ter)Pathogenic
1710463NM_152641.4(ARID2):c.2767C>T (p.Gln923Ter)Pathogenic
1711363GRCh37/hg19 12q12(chr12:46230372-46233279)x1Pathogenic
1802698NM_152641.4(ARID2):c.1837C>T (p.Gln613Ter)Pathogenic
1805865NM_152641.4(ARID2):c.1334_1338del (p.Met445fs)Pathogenic
1879230NM_152641.4(ARID2):c.2164dup (p.Ser722fs)Pathogenic
1879231NM_152641.4(ARID2):c.3467del (p.Ile1156fs)Pathogenic

SpliceAI

3962 predictions. Top by Δscore:

VariantEffectΔscore
12:45729925:GAGG:Gdonor_gain1.0000
12:45729927:GG:Gdonor_gain1.0000
12:45729928:GG:Gdonor_gain1.0000
12:45729929:G:GAdonor_loss1.0000
12:45729929:G:GGdonor_gain1.0000
12:45730134:GAAG:Gdonor_gain1.0000
12:45730136:AGG:Adonor_loss1.0000
12:45730138:G:GAdonor_loss1.0000
12:45811414:TCAGT:Tacceptor_loss1.0000
12:45811415:CAGTT:Cacceptor_loss1.0000
12:45811416:A:AGacceptor_gain1.0000
12:45811416:AG:Aacceptor_loss1.0000
12:45811417:G:GGacceptor_gain1.0000
12:45811417:GTT:Gacceptor_gain1.0000
12:45811550:GG:Gdonor_gain1.0000
12:45811551:GG:Gdonor_gain1.0000
12:45817668:A:AGacceptor_gain1.0000
12:45817669:G:GGacceptor_gain1.0000
12:45817669:GATT:Gacceptor_gain1.0000
12:45817884:CGACA:Cdonor_gain1.0000
12:45817885:GACA:Gdonor_gain1.0000
12:45817885:GACAG:Gdonor_gain1.0000
12:45817886:ACA:Adonor_gain1.0000
12:45817887:CA:Cdonor_gain1.0000
12:45817887:CAG:Cdonor_loss1.0000
12:45817888:AG:Adonor_loss1.0000
12:45817889:G:Adonor_loss1.0000
12:45817889:G:GGdonor_gain1.0000
12:45817890:T:Adonor_loss1.0000
12:45817891:AA:Adonor_loss1.0000

AlphaMissense

11927 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:45729891:T:CF19L1.000
12:45729892:T:CF19S1.000
12:45729893:C:AF19L1.000
12:45729893:C:GF19L1.000
12:45729904:T:CL23P1.000
12:45729912:T:CF26L1.000
12:45729913:T:CF26S1.000
12:45729914:C:AF26L1.000
12:45729914:C:GF26L1.000
12:45729915:C:GH27D1.000
12:45730085:T:CL45P1.000
12:45730100:T:CL50P1.000
12:45730102:T:GY51D1.000
12:45730112:T:AV54D1.000
12:45730127:G:AG59E1.000
12:45731218:T:AV63D1.000
12:45731235:T:AW69R1.000
12:45731235:T:CW69R1.000
12:45731236:G:CW69S1.000
12:45731237:G:CW69C1.000
12:45731237:G:TW69C1.000
12:45731307:T:GY93D1.000
12:45811423:T:AL97Q1.000
12:45811423:T:CL97P1.000
12:45811431:T:GY100D1.000
12:45811432:A:CY100S1.000
12:45811436:G:CE101D1.000
12:45811436:G:TE101D1.000
12:45817733:T:CL161S1.000
12:45817745:T:CL165P1.000

dbSNP variants (sampled 300 via entrez): RS1000000554 (12:45832706 A>G), RS1000013070 (12:45878537 A>G), RS1000019278 (12:45848386 T>C,G), RS1000040257 (12:45824685 G>C), RS1000113455 (12:45750272 C>G,T), RS1000140169 (12:45781876 G>A), RS1000151069 (12:45824421 A>T), RS1000164772 (12:45880033 T>C), RS1000165902 (12:45853833 G>A), RS1000172394 (12:45788341 G>A), RS1000188408 (12:45898096 C>A), RS1000204008 (12:45905277 A>G), RS1000217964 (12:45860614 A>C,G), RS1000218482 (12:45830822 C>A,T), RS1000242878 (12:45813826 G>A)

Disease associations

OMIM: gene MIM:609539 | disease phenotypes: MIM:617808, MIM:135900, MIM:609943, MIM:614562, MIM:619681

GenCC curated gene-disease

DiseaseClassificationInheritance
Coffin-Siris syndromeStrongAutosomal dominant
Coffin-Siris syndrome 6StrongAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Coffin-Siris syndromeDefinitiveAD

Mondo (10): Coffin-Siris syndrome 6 (MONDO:0033492), neurodevelopmental disorder (MONDO:0700092), chronic diarrheal disease (MONDO:0044751), microcephaly (MONDO:0001149), Coffin-Siris syndrome (MONDO:0015452), desmoplastic/nodular medulloblastoma (MONDO:0016711), autism spectrum disorder (MONDO:0005258), Coffin-Siris syndrome 1 (MONDO:0007617), dystonia, early-onset, and/or spastic paraplegia (MONDO:0859215), Castleman-Kojima disease (MONDO:0018702)

Orphanet (4): Coffin-Siris syndrome (Orphanet:1465), Desmoplastic/nodular medulloblastoma (Orphanet:251863), TAFRO syndrome (Orphanet:457077), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

103 total (30 of 103 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000028Cryptorchidism
HP:0000047Hypospadias
HP:0000085Horseshoe kidney
HP:0000119Abnormality of the genitourinary system
HP:0000154Wide mouth
HP:0000175Cleft palate
HP:0000179Thick lower lip vermilion
HP:0000219Thin upper lip vermilion
HP:0000252Microcephaly
HP:0000278Retrognathia
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000289Broad philtrum
HP:0000294Low anterior hairline
HP:0000322Short philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000358Posteriorly rotated ears
HP:0000365Hearing impairment
HP:0000369Low-set ears
HP:0000405Conductive hearing impairment
HP:0000455Broad nasal tip
HP:0000463Anteverted nares
HP:0000486Strabismus
HP:0000494Downslanted palpebral fissures
HP:0000505Visual impairment
HP:0000508Ptosis
HP:0000545Myopia
HP:0000574Thick eyebrow

GWAS associations

16 associations (top):

StudyTraitp-value
GCST000461_8Hippocampal atrophy8.000000e-06
GCST005316_367Intelligence (MTAG)2.000000e-08
GCST006291_122Spherical equivalent or myopia (age of diagnosis)7.000000e-15
GCST006613_83Triglycerides6.000000e-11
GCST007565_168Morning person5.000000e-17
GCST007565_34Morning person8.000000e-17
GCST007576_341Chronotype5.000000e-17
GCST010002_216Refractive error2.000000e-29
GCST010142_31Fish- and plant-related diet7.000000e-09
GCST010244_377Triglyceride levels9.000000e-11
GCST010320_91PR interval2.000000e-09
GCST010321_72PR interval2.000000e-10
GCST90002383_1Hematocrit1.000000e-14
GCST90002384_305Hemoglobin4.000000e-12
GCST90002390_56Mean corpuscular hemoglobin3.000000e-09
GCST90002403_447Red blood cell count5.000000e-18

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0005039hippocampal atrophy
EFO:0004337intelligence
EFO:0004847age at onset
EFO:0004530triglyceride measurement
EFO:0008328chronotype measurement
EFO:0008111diet measurement
EFO:0004462PR interval
EFO:0004348hematocrit
EFO:0004509hemoglobin measurement
EFO:0004527mean corpuscular hemoglobin
EFO:0004305erythrocyte count

MeSH disease descriptors (3)

DescriptorNameTree numbers
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
D065886Neurodevelopmental DisordersF03.625
C536436Coffin-Siris syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725016 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.32Kd4847nMCHEMBL5653589
5.30ED505023nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 8 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2147887: Binding affinity to human ARID2 incubated for 45 mins by Kinobead based pull down assaykd4.8469uM

CTD chemical–gene interactions

47 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases methylation, increases expression, affects cotreatment, decreases expression, affects expression10
trichostatin Adecreases expression, affects expression, affects cotreatment4
bisphenol Aaffects methylation, increases expression, increases methylation2
(+)-JQ1 compoundaffects expression, increases reaction, decreases expression2
Benzo(a)pyreneaffects methylation, increases mutagenesis2
Formaldehydedecreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Aflatoxin B1decreases methylation, increases methylation2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, decreases expression1
TAK-243decreases sumoylation1
methylmercuric chloridedecreases expression1
lasiocarpinedecreases expression, increases metabolic processing1
triphenyl phosphateaffects expression1
riddelliinedecreases expression, increases metabolic processing1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2affects methylation1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
Irinotecandecreases expression1
Sunitinibdecreases expression1
Zoledronic Aciddecreases expression1
Panobinostataffects expression, increases reaction1
Acetaminophenincreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5650929BindingBinding affinity to human ARID2 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

486 cell lines: 464 induced pluripotent stem cell, 12 cancer cell line, 7 transformed cell line, 3 telomerase immortalized cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_1105CAL-12TCancer cell lineMale
CVCL_1134COLO 792Cancer cell lineMale
CVCL_3947SNU-354Cancer cell lineMale
CVCL_9S58HPSI0114i-kolf_2-C1Induced pluripotent stem cellMale
CVCL_A4IICAL-12T KRAS (G12C/+)Cancer cell lineMale
CVCL_AE29HPSI0114i-kolf_2Induced pluripotent stem cellMale
CVCL_B1JYAbcam HeLa ARID2 KOCancer cell lineFemale
CVCL_B5P3KOLF2.1JInduced pluripotent stem cellMale
CVCL_B7JKSCLC-J1Cancer cell lineMale
CVCL_C7TYKOLF2.1J PPM1H KOInduced pluripotent stem cellMale

Clinical trials (associated diseases)

229 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT03876717PHASE4COMPLETEDEffect of the Sequestrant Colesevelam in Bile Acid Diarrhoea
NCT07436104PHASE4COMPLETEDMortality Control Program for Economically Productive Age Group in Tribal Area of Melghat.
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT01585025PHASE2COMPLETEDObeticholic Acid in Bile Acid Diarrhoea
NCT03270085PHASE2COMPLETEDTrial to Understand Efficacy of Colesevelam in Diarrhea Predominant IBS Patients With Bile Acid Malabsorption
NCT05130047PHASE2COMPLETEDAldafermin (NGM282) for Chronic Diarrhea Due to Bile Acid Malabsorption (BAM)
NCT05690321PHASE2COMPLETEDOpium Tincture Against Chronic Diarrhea - Patients
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT06960369PHASE1RECRUITINGEfficacy of Repeated Transcranial Magnetic Stimulation Combined With a Live Probiotic Tablet (Combined Bifidobacterium, Lactobacillus, Enterococcus and Bacillus Cereus Tablets, Live) in Diarrhea-Predominant Irritable Bowel Syndrome (IBS-D)
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385PHASE2/PHASE3RECRUITINGFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098EARLY_PHASE1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedACTIVE_NOT_RECRUITINGEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293Not specifiedCOMPLETEDn-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644Not specifiedCOMPLETEDImproving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991Not specifiedUNKNOWNEarly Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers